Introduction to spatiotemporal modeling and simulation
This course teaches modeling techniques for spatially resolved systems. You will learn to account for the geometry of a system and for transport in space. After repetition of the basics from mathematics and physics, you will model processes such as diffusion and flow, and simulate them in the computer.
Contents
dimensionality analysis, causality diagrams, vector fields, particle methods, governing equations for diffusion and flow, hybrid particlemesh methods for computer simulations, student project: simulation of a biological system.
Time/Place
Summer Term
Lecture: Tuesdays, 14:5016:20h, CSBD Seminar Room Ground Floor (Pfotenhauerstr. 108)
Exercises: Tuesdays, 16:4018:10h, CSBD Seminar Room Ground Floor (Pfotenhauerstr. 108)
NO LECTURE / NO EXERCISE ON: MAY 21, 2019.
Format
2 SWS lecture, 2 SWS exercise, selfstudy
Programs / Modules
M.Sc. Computational Modeling and Simulation, Modules: CMSCLSMOS
B.Sc. Computer Science, Module: INFB510
Diplom Computer Science, Module: INFD510
Registration to the course
For students of the Master program "Computational Modeling and Simulation: via CampusNet SELMA
For students of the Computer Science programs: via jExam
For students of the IMPRSCellDevoSys: via the program office
Teachers
Lecture: Prof. Ivo F. Sbalzarini
Exercises: Aryaman Gupta
Exam
Date/Time: August 9, 2019 / 9am11am
Place: APB/E005 and APB/E006
Format: written
Duration: 120 minutes
At the exam, the following may be used:
 4 A4 sheets (8 pages if you print duplex) of handwritten summary. We recommend writing the summary by hand, but it can also be machinewritten. In the latter case, the font size must be 8 points or larger throughout.
 A standard pocket calculator (devices with network or bluetooth access, as well as devices capable of storing and displaying documents are not allowed)
Registration to the exam
For students of the Master program "Computational Modeling and Simulation: via CampusNet SELMA
For students of the Computer Science programs: via lists circulated in the lecture, or via email to Prof. Sbalzarini
For students of the IMPRSCellDevoSys: via lists circulated in the lecture, or via email to Prof. Sbalzarini
Exam Review
You can come and look at your exam, and ask questions about its correction and the answers given during the following times:
 November 1, 2019, 1pm2pm, CSBD Seminar Room Ground Floor (Pfotenhauerstr. 108)
 November 4, 2019, 10am11am, APB/1005 (Computer Science building)
 November 7, 2019, 4pm5pm, CSBD121 (Pfotenhauerstr. 108)
Learning goals

Analysis of the dynamic behavior of biological or physical systems with spatial structure

Formulation of a model of the system behavior

Computer simulation of the model using numerical methods
We focus on biological systems. The taught methods and concepts are, however, applicable in a much broader sense.
Lecture language: ENGLISH
Please find below the lecture syllabus, the slides, the selfcheck questions, and the exercises:
 Lecture 1  Administration and Introduction (Slides PDF, Handouts PDF, Slides Intro PDF, Handouts Intro PDF, Selftest questions PDF)
 Lecture 2  Dimensional Analysis (Slides PDF, Handouts PDF, Selftest questions PDF, Exercise PDF, Solution PDF)
 Lecture 3  Modeling Dynamics: Reservoirs and Flows (Slides PDF, Handouts PDF, Selftest questions PDF, Exercise PDF, Solution PDF, Additional Reading on ODE solving)
 Lecture 4  Recap on Vector Calculus (Slides PDF, Handouts PDF, Selftest questions PDF, Exercise PDF, Solution PDF)
 Lecture 5  Conservation Laws and Control Volume Methods (Slides PDF, Handouts PDF, Selftest questions PDF, Exercise PDF, Solution PDF)
 Lecture 6  Particle Methods (Slides PDF, Handouts PDF, Selftest questions PDF, Exercise PDF, QSBacterialPos DAT, Solution ZIP)
 Lecture 7  Diffusion (Slides PDF, Handouts PDF, Selftest questions PDF, Exercise PDF, Solution ZIP)
 Lecture 8  ReactionDiffusion (Slides PDF, Handouts PDF, Selftest questions PDF, Exercise PDF, Solution ZIP)
 Lecture 9  AdvectionDiffusion (Slides PDF, Handouts PDF, Selftest questions PDF, Exercise PDF, bacterialPos.dat, Solution ZIP)
 Lecture 10  Flow (Slides PDF, Handouts PDF, Selftest questions PDF, Exercise PDF, Solution ZIP)
 Lecture 11  PDEs (Slides PDF, Handouts PDF, Selftest questions PDF, Exercise PDF, Solution ZIP, Additional Reading on 2nd order differential equations)
 Lecture 12  Bonus: Waves (Slides PDF, Handouts PDF, Selftest questions PDF)
Full lecture notes can be found here: Script (PDF).
Project
The student project will aim at implementing the Quorum Sensing model proposed by J. Müller et al. as described in this publicly available preprint. The final version of the paper is available from Springer Link with university access.